# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 #' ArvadosFile #' #' ArvadosFile class represents a file inside Arvados collection. #' #' @section Usage: #' \preformatted{file = ArvadosFile$new(name)} #' #' @section Arguments: #' \describe{ #' \item{name}{Name of the file.} #' } #' #' @section Methods: #' \describe{ #' \item{getName()}{Returns name of the file.} #' \item{getRelativePath()}{Returns file path relative to the root.} #' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.} #' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).} #' \item{connection(rw)}{Get connection opened in "read" or "write" mode.} #' \item{flush()}{Write connections content to a file (override current content of the file).} #' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.} #' \item{getSizeInBytes()}{Returns file size in bytes.} #' \item{move(destination)}{Moves file to a new location inside collection.} #' \item{copy(destination)}{Copies file to a new location inside collection.} #' } #' #' @name ArvadosFile #' @examples #' \dontrun{ #' myFile <- ArvadosFile$new("myFile") #' #' myFile$write("This is new file content") #' fileContent <- myFile$read() #' fileContent <- myFile$read("text") #' fileContent <- myFile$read("raw", offset = 8, length = 4) #' #' #Write a table: #' arvConnection <- myFile$connection("w") #' write.table(mytable, arvConnection) #' arvadosFile$flush() #' #' #Read a table: #' arvConnection <- myFile$connection("r") #' mytable <- read.table(arvConnection) #' #' myFile$move("newFolder/myFile") #' myFile$copy("newFolder/myFile") #' } NULL #' @export ArvadosFile <- R6::R6Class( "ArvadosFile", public = list( initialize = function(name) { if(name == "") stop("Invalid name.") private$name <- name }, getName = function() private$name, getFileListing = function(fullpath = TRUE) { self$getName() }, getSizeInBytes = function() { if(is.null(private$collection)) return(0) REST <- private$collection$getRESTService() fileSize <- REST$getResourceSize(self$getRelativePath(), private$collection$uuid) fileSize }, get = function(fileLikeObjectName) { return(NULL) }, getFirst = function() { return(NULL) }, getCollection = function() private$collection, setCollection = function(collection, setRecursively = TRUE) { private$collection <- collection }, getRelativePath = function() { relativePath <- c(private$name) parent <- private$parent while(!is.null(parent)) { relativePath <- c(parent$getName(), relativePath) parent <- parent$getParent() } relativePath <- relativePath[relativePath != ""] paste0(relativePath, collapse = "/") }, getParent = function() private$parent, setParent = function(newParent) private$parent <- newParent, read = function(contentType = "raw", offset = 0, length = 0) { if(is.null(private$collection)) stop("ArvadosFile doesn't belong to any collection.") if(offset < 0 || length < 0) stop("Offset and length must be positive values.") REST <- private$collection$getRESTService() fileContent <- REST$read(self$getRelativePath(), private$collection$uuid, contentType, offset, length) fileContent }, connection = function(rw) { if (rw == "r" || rw == "rb") { REST <- private$collection$getRESTService() return(REST$getConnection(self$getRelativePath(), private$collection$uuid, rw)) } else if (rw == "w") { private$buffer <- textConnection(NULL, "w") return(private$buffer) } }, flush = function() { v <- textConnectionValue(private$buffer) close(private$buffer) self$write(paste(v, collapse='\n')) }, write = function(content, contentType = "text/html") { if(is.null(private$collection)) stop("ArvadosFile doesn't belong to any collection.") REST <- private$collection$getRESTService() writeResult <- REST$write(self$getRelativePath(), private$collection$uuid, content, contentType) writeResult }, move = function(destination) { if(is.null(private$collection)) stop("ArvadosFile doesn't belong to any collection.") destination <- trimFromEnd(destination, "/") nameAndPath <- splitToPathAndName(destination) newParent <- private$collection$get(nameAndPath$path) if(is.null(newParent)) stop("Unable to get destination subcollection.") childWithSameName <- newParent$get(nameAndPath$name) if(!is.null(childWithSameName)) stop("Destination already contains content with same name.") REST <- private$collection$getRESTService() REST$move(self$getRelativePath(), paste0(newParent$getRelativePath(), "/", nameAndPath$name), private$collection$uuid) private$dettachFromCurrentParent() private$attachToNewParent(self, newParent) private$parent <- newParent private$name <- nameAndPath$name self }, copy = function(destination) { if(is.null(private$collection)) stop("ArvadosFile doesn't belong to any collection.") destination <- trimFromEnd(destination, "/") nameAndPath <- splitToPathAndName(destination) newParent <- private$collection$get(nameAndPath$path) if(is.null(newParent)) stop("Unable to get destination subcollection.") childWithSameName <- newParent$get(nameAndPath$name) if(!is.null(childWithSameName)) stop("Destination already contains content with same name.") REST <- private$collection$getRESTService() REST$copy(self$getRelativePath(), paste0(newParent$getRelativePath(), "/", nameAndPath$name), private$collection$uuid) newFile <- self$duplicate(nameAndPath$name) newFile$setCollection(self$getCollection()) private$attachToNewParent(newFile, newParent) newFile$setParent(newParent) newFile }, duplicate = function(newName = NULL) { name <- if(!is.null(newName)) newName else private$name newFile <- ArvadosFile$new(name) newFile } ), private = list( name = NULL, size = NULL, parent = NULL, collection = NULL, buffer = NULL, attachToNewParent = function(content, newParent) { # We temporary set parents collection to NULL. This will ensure that # add method doesn't post this file on REST. # We also need to set content's collection to NULL because # add method throws exception if we try to add content that already # belongs to a collection. parentsCollection <- newParent$getCollection() content$setCollection(NULL, setRecursively = FALSE) newParent$setCollection(NULL, setRecursively = FALSE) newParent$add(content) content$setCollection(parentsCollection, setRecursively = FALSE) newParent$setCollection(parentsCollection, setRecursively = FALSE) }, dettachFromCurrentParent = function() { # We temporary set parents collection to NULL. This will ensure that # remove method doesn't remove this file from REST. parent <- private$parent parentsCollection <- parent$getCollection() parent$setCollection(NULL, setRecursively = FALSE) parent$remove(private$name) parent$setCollection(parentsCollection, setRecursively = FALSE) } ), cloneable = FALSE ) #' print.ArvadosFile #' #' Custom print function for ArvadosFile class #' #' @param x Instance of ArvadosFile class #' @param ... Optional arguments. #' @export print.ArvadosFile = function(x, ...) { collection <- NULL relativePath <- x$getRelativePath() if(!is.null(x$getCollection())) { collection <- x$getCollection()$uuid relativePath <- paste0("/", relativePath) } cat(paste0("Type: ", "\"", "ArvadosFile", "\""), sep = "\n") cat(paste0("Name: ", "\"", x$getName(), "\""), sep = "\n") cat(paste0("Relative path: ", "\"", relativePath, "\""), sep = "\n") cat(paste0("Collection: ", "\"", collection, "\""), sep = "\n") }